Sonia Bermudez, current manager of the women's Under-23 side, has been named as her successor.
Tome, who took over the role less than two years ago, had previously served as assistant coach to Jorge Vilda from 2018 until his dismissal in 2023.
Despite guiding Spain to the European Championship final in Switzerland last month, the RFEF decided against renewing Tome's contract. She previously led Spain to the 2023-24 Nations League title.
However, a disappointing campaign at the Paris Olympics where the team failed to secure a medal followed by the penalty shootout heartbreak at the Euros, undermined confidence in her leadership.
"The Board of Directors... would like to thank Montse Tome for her work, professionalism and dedication in various roles during her time as a member of the national teams at the RFEF, particularly during her time as head coach of the senior women's national team," the RFEF said in a statement.